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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
2qf7
Jmol
Contents
Protein chains
1076 a.a. *
1017 a.a. *
Ligands
COA
SAP ×2
GOL
FMT ×2
Metals
_MG ×6
_ZN ×2
_CL ×4
Waters ×1318
* Residue conservation analysis
PDB id:
2qf7
Name: Ligase
Title: Crystal structure of a complete multifunctional pyruvate car from rhizobium etli
Structure: Pyruvate carboxylase protein. Chain: a, b. Engineered: yes
Source: Rhizobium etli. Organism_taxid: 347834. Strain: cfn 42. Gene: pyc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.180     R-free:   0.223
Authors: M.St Maurice,K.H.Surinya,I.Rayment
Key ref:
M.St Maurice et al. (2007). Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme. Science, 317, 1076-1079. PubMed id: 17717183 DOI: 10.1126/science.1144504
Date:
27-Jun-07     Release date:   04-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q2K340  (Q2K340_RHIEC) -  Pyruvate carboxylase protein
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1154 a.a.
1076 a.a.*
Protein chain
Pfam   ArchSchema ?
Q2K340  (Q2K340_RHIEC) -  Pyruvate carboxylase protein
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1154 a.a.
1017 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.6.4.1.1  - Pyruvate carboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate
ATP
Bound ligand (Het Group name = SAP)
matches with 93.75% similarity 		+
pyruvate
Bound ligand (Het Group name = GOL)
matches with 71.43% similarity 		+
HCO(3)(-)
Bound ligand (Het Group name = FMT)
matches with 75.00% similarity 		=
ADP
Bound ligand (Het Group name = COA)
matches with 84.38% similarity 		+ phosphate
 + oxaloacetate
      Cofactor: Biotin; Zinc or manganese
Biotin
 Zinc
 or manganese
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.1144504 Science 317:1076-1079 (2007)
PubMed id: 17717183  
 
 
Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.
M.St Maurice, L.Reinhardt, K.H.Surinya, P.V.Attwood, J.C.Wallace, W.W.Cleland, I.Rayment.
 
  ABSTRACT  
 
Biotin-dependent multifunctional enzymes carry out metabolically important carboxyl group transfer reactions and are potential targets for the treatment of obesity and type 2 diabetes. These enzymes use a tethered biotin cofactor to carry an activated carboxyl group between distantly spaced active sites. The mechanism of this transfer has remained poorly understood. Here we report the complete structure of pyruvate carboxylase at 2.0 angstroms resolution, which shows its domain arrangement. The structure, when combined with mutagenic analysis, shows that intermediate transfer occurs between active sites on separate polypeptide chains. In addition, domain rearrangements associated with activator binding decrease the distance between active-site pairs, providing a mechanism for allosteric activation. This description provides insight into the function of biotin-dependent enzymes and presents a new paradigm for multifunctional enzyme catalysis.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. (A) Schematic drawing of the primary structure arrangement for the multidomain PC from R. etli. The allosteric domain, indicated with asterisks, includes residues 471 to 489 and 1002 to 1073. (B) The structure of the R. etli PC monomer A. The BC,CT, BCCP, and allosteric domains are colored blue, yellow, red, and green, respectively. The chemical reactions catalyzed in the individual domains are illustrated below the corresponding domain structure. ADP, adenosine diphosphate; P[i], inorganic phosphate. 		Figure 2.
Fig. 2. (A) The ATP binding site. The revised definition of the precise ATP binding site reveals several interacting residues not previously noted in the structure of the BC subunit from ACC. In particular, the interaction of Lys^245 with the -phosphate of ATP is consistent with substrate-labeling studies that suggest that this residue directly interacts with ATP (30). Several previously unrecognized residues, including Glu^283, Glu^297, and Asn^299, are now seen to be important for coordinating the two essential Mg^2+ ions (depicted as green spheres) and ATP binding. (B) The ethyl-CoA binding site. Interactions with the nucleotide portion of ethyl-CoA include residues from both BC subunits and from the allosteric domain. Most notably, Arg^472 of the allosteric domain creates a strong interaction with the 5' -phosphate of ethyl-CoA.
 
  The above figures are reprinted by permission from the AAAs: Science (2007, 317, 1076-1079) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21426897 A.Adina-Zada, R.Hazra, C.Sereeruk, S.Jitrapakdee, T.N.Zeczycki, M.S.Maurice, W.W.Cleland, J.C.Wallace, and P.V.Attwood (2011).
Probing the allosteric activation of pyruvate carboxylase using 2',3'-O-(2,4,6-trinitrophenyl) adenosine 5'-triphosphate as a fluorescent mimic of the allosteric activator acetyl CoA.
  Arch Biochem Biophys, 509, 117-126.  
21479798 M.F.Dunn (2011).
Anaplerotic Function of Phosphoenolpyruvate Carboxylase in Bradyrhizobium japonicum USDA110.
  Curr Microbiol, 62, 1782-1788.  
20725044 C.S.Huang, K.Sadre-Bazzaz, Y.Shen, B.Deng, Z.H.Zhou, and L.Tong (2010).
Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.
  Nature, 466, 1001-1005.
PDB code: 3n6r
20552640 J.C.Wallace (2010).
My favorite pyruvate carboxylase.
  IUBMB Life, 62, 535-538.  
20230056 S.Duangpan, S.Jitrapakdee, A.Adina-Zada, L.Byrne, T.N.Zeczycki, M.St Maurice, W.W.Cleland, J.C.Wallace, and P.V.Attwood (2010).
Probing the catalytic roles of Arg548 and Gln552 in the carboxyl transferase domain of the Rhizobium etli pyruvate carboxylase by site-directed mutagenesis.
  Biochemistry, 49, 3296-3304.  
19213731 C.Y.Chou, L.P.Yu, and L.Tong (2009).
Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.
  J Biol Chem, 284, 11690-11697.
PDB codes: 3g8c 3g8d
19523900 L.P.Yu, S.Xiang, G.Lasso, D.Gil, M.Valle, and L.Tong (2009).
A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A.
  Structure, 17, 823-832.
PDB codes: 3hb9 3hbl 3ho8
19341298 T.N.Zeczycki, M.St Maurice, S.Jitrapakdee, J.C.Wallace, P.V.Attwood, and W.W.Cleland (2009).
Insight into the carboxyl transferase domain mechanism of pyruvate carboxylase from Rhizobium etli.
  Biochemistry, 48, 4305-4313.  
18272421 A.Adina-Zada, S.Jitrapakdee, K.H.Surinya, M.J.McIldowie, M.J.Piggott, W.W.Cleland, J.C.Wallace, and P.V.Attwood (2008).
Insights into the mechanism and regulation of pyruvate carboxylase by characterisation of a biotin-deficient mutant of the Bacillus thermodenitrificans enzyme.
  Int J Biochem Cell Biol, 40, 1743-1752.  
18620418 A.S.Reger, R.Wu, D.Dunaway-Mariano, and A.M.Gulick (2008).
Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase.
  Biochemistry, 47, 8016-8025.
PDB codes: 3cw8 3cw9
18725455 I.Mochalkin, J.R.Miller, A.Evdokimov, S.Lightle, C.Yan, C.K.Stover, and G.L.Waldrop (2008).
Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
  Protein Sci, 17, 1706-1718.
PDB codes: 2c00 2j9g 2vpq 2vqd 2vr1
18469096 J.A.Aguilar, C.Díaz-Pérez, A.L.Díaz-Pérez, J.S.Rodríguez-Zavala, B.J.Nikolau, and J.Campos-García (2008).
Substrate specificity of the 3-methylcrotonyl coenzyme A (CoA) and geranyl-CoA carboxylases from Pseudomonas aeruginosa.
  J Bacteriol, 190, 4888-4893.  
18613815 S.Jitrapakdee, M.St Maurice, I.Rayment, W.W.Cleland, J.C.Wallace, and P.V.Attwood (2008).
Structure, mechanism and regulation of pyruvate carboxylase.
  Biochem J, 413, 369-387.  
18297087 S.Xiang, and L.Tong (2008).
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
  Nat Struct Mol Biol, 15, 295-302.
PDB codes: 3bg3 3bg5 3bg9
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.